Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

Koltes, J. E.; Fritz-Waters, E.; Eisley, C. J.; Choi, I.; Bao, H.; Kommadath, A.; Serão, N. V. L.; Boddicker, N. J.; Abrams, S. M.; Schroyen, Martine; Loyd, H.; Tuggle, C. K.; Plastow, G. S.; Guan, L.; Stothard, P.; Lunney, J. K.; Liu, P.; Carpenter, S.; Rowland, R. R. R.; Dekkers, J. C. M.; Reecy, J. M.

doi:10.1186/s12864-015-1635-9

Article (Scientific journals)

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

Koltes, J. E.; Fritz-Waters, E.; Eisley, C. J. et al.

2015 • In BMC Genomics, 16 (1)

Peer Reviewed verified by ORBi

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https://hdl.handle.net/2268/209884

DOI
10.1186/s12864-015-1635-9

PubMed
26016888

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Keywords :

Article; GBP5 gene; Porcine reproductive and respiratory syndrome virus; Porcine respiratory and reproductive syndrome virus; Suidae; Sus scrofa

Abstract :

[en] Background: Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4). Results: Within this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100 % concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype. Conclusions: GBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV. © 2015 Koltes et al.

Disciplines :

Genetics & genetic processes

Author, co-author :

Koltes, J. E.; Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, United States

Fritz-Waters, E.; Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, United States

Eisley, C. J.; Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, United States, Department of Statistics, Iowa State University, 1121 Snedecor Hall, Ames, IA, United States

Choi, I.; USDA-ARS, BARC, APDL, Building 1040, Beltsville, MD, United States

Bao, H.; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada

Kommadath, A.; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada

Serão, N. V. L.; Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, United States

Boddicker, N. J.; Genesus Inc, 101 2nd Street, Oakville, MB, Canada

Abrams, S. M.; USDA-ARS, BARC, APDL, Building 1040, Beltsville, MD, United States

Schroyen, Martine ; Université de Liège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Zootechnie

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Title :

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

Publication date :

2015

Journal title :

BMC Genomics

eISSN :

1471-2164

Publisher :

BioMed Central Ltd.

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Issue :

Peer reviewed :

Peer Reviewed verified by ORBi

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since 24 April 2017

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